rs17587144

Variant names:

• chr4-40501253-G-A
• rs17587144
• NM_001098634.2:c.-154-34554C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001098634.2(RBM47):​c.-154-34554C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 152,252 control chromosomes in the GnomAD database, including 149 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.034 (149 hom., cov: 32)
• Consequence: RBM47 NM_001098634.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 2 publications found

Genes affected

RBM47 (HGNC:30358): (RNA binding motif protein 47) Enables RNA binding activity. Predicted to act upstream of or within cytidine to uridine editing and hematopoietic progenitor cell differentiation. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM47	NM_001098634.2	c.-154-34554C>T		intron_variant	Intron 2 of 6	ENST00000295971.12	NP_001092104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM47	ENST00000295971.12	c.-154-34554C>T		intron_variant	Intron 2 of 6	5	NM_001098634.2	ENSP00000295971.7

Frequencies

GnomAD3 genomes AF: 0.0342 AC: 5199 AN: 152134 Hom.: 147 Cov.: 32

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0525

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0352

Gnomad OTH AF: 0.0335

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0342 AC: 5205 AN: 152252 Hom.: 149 Cov.: 32 AF XY: 0.0357 AC XY: 2658 AN XY: 74436

African (AFR) AF: 0.0113 AC: 469 AN: 41564

American (AMR) AF: 0.0350 AC: 535 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0525 AC: 182 AN: 3466

East Asian (EAS) AF: 0.166 AC: 856 AN: 5170

South Asian (SAS) AF: 0.0437 AC: 211 AN: 4824

European-Finnish (FIN) AF: 0.0437 AC: 463 AN: 10590

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0352 AC: 2391 AN: 68022

Other (OTH) AF: 0.0383 AC: 81 AN: 2114

Alfa AF: 0.0363 Hom.: 20

Bravo AF: 0.0347

Asia WGS AF: 0.0960 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.67
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17587144; hg19: chr4-40503270;